The Systems Biology Simulation Core Library

Bioinformatics. 2021 Sep 23;btab669. doi: 10.1093/bioinformatics/btab669. Online ahead of print.

Abstract

Summary: Studying biological systems generally relies on computational modelling and simulation, e.g., model-driven discovery and hypothesis testing. Progress in standardisation efforts led to the development of interrelated file formats to exchange and reuse models in systems biology, such as SBML, the Simulation Experiment Description Markup Language (SED-ML), or the Open Modeling EXchange format (OMEX). Conducting simulation experiments based on these formats requires efficient and reusable implementations to make them accessible to the broader scientific community and to ensure the reproducibility of the results. The Systems Biology Simulation Core Library (SBSCL) provides interpreters and solvers for these standards as a versatile open-source API in JavaTM. The library simulates even complex bio-models and supports deterministic Ordinary Differential Equations (ODEs); Stochastic Differential Equations (SDEs); constraint-based analyses; recent SBML and SED-ML versions; exchange of results, and visualisation of in silico experiments; open modelling exchange formats (COMBINE archives); hierarchically structured models; and compatibility with standard testing systems, including the Systems Biology Test Suite and published models from the BioModels and BiGG databases.

Availability: SBSCL is freely available at https://draeger-lab.github.io/SBSCL/ and via Maven Central.

Supplementary information: The material available at Bioinformatics online provides details on resources and availability, implementation, support of the SBML Test Suite, BioModels, and BiGG simulations with benchmark comparisons, and comparison to other simulators with SBML support.